Kazutoshi Yoshitake

Omitting end preparation reduces index misassignment in Nanopore-based DNA metabarcoding: application to a decadal coastal time series in the Sea of Okhotsk

The paper develops a workflow to reduce index misassignment in Nanopore-based eDNA metabarcoding, applied to a decadal coastal time series showing seasonal fish taxa patterns.

Chromosome-scale genome assembly of Cycas revoluta provides insights into cycad diversification and species diversity

The paper presents a chromosome-scale genome assembly of Cycas revoluta and identifies genes related to sex determination and thermogenesis, offering insights into cycad diversification.

Gluconeogenesis and glycogen metabolism in the epidermis and endoderm of Xenopus tropicalis embryos and larvae.

This study identifies gluconeogenesis in the epidermis and endoderm of Xenopus tropicalis embryos, showing its role in development and highlighting tissue-specific metabolic diversity.

Oribatid Mites Supply Tetrodotoxin to Poisonous Newts

This study identifies oribatid mites as the primary dietary source of tetrodotoxin for Japanese fire-bellied newts and shows that newts sequester TTX from these mites.

Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies

This study presents a chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping, revealing a genome twice the size of Arabidopsis thaliana.

The minimal endosymbiosis between Spurilla braziliana (Aeolidiidae, Nudibranchia) and Symbiodiniaceae

This study examines the algal symbiosis in Spurilla braziliana, finding limited morphological adaptations and absence of associated bacteria, suggesting a primitive symbiotic state.

Environmental exosomes: Evidence of extracellular RNA release by aquatic organisms

The paper identifies that pearl oysters release exosomes containing species-specific RNA into the environment, suggesting a new role for aquatic exosomes in inter-organismal communication and ecological monitoring.

Development of a Comprehensive Analytical Workflow for eDNA Analysis of Vertebrates, Arthropods, and Mollusks

This paper develops an eDNA analysis workflow using long-read sequencing and expanded databases to improve detection of vertebrates, arthropods, and mollusks.

The Greenland shark genome: insights into deep-sea ecology and lifespan extremes

This paper presents the first chromosome-level genome assembly of the Greenland shark, identifying genetic features associated with its extreme longevity and deep-sea adaptations.

Symbiotic Bacterial Partners for Chemical Defense are Vertically Transmitted in a Marine Sponge

This study identifies vertical transmission of cytotoxin-producing bacteria in marine sponges through bacteriocyte-like structures.

The complete mitochondrial genome of Spurilla braziliana MacFarland 1909 (Nudibranchia, Aeolidiidae).

This study sequenced and analyzed the complete mitochondrial genome of Spurilla braziliana, revealing its phylogenetic placement within the Aeolidioidea superfamily.

A novel monocarboxylate transporter involved in 3-hydroxykynurenine transport for ommochrome coloration

This study identifies a novel monocarboxylate transporter, 3OHKT, responsible for 3-hydroxykynurenine uptake in ommochrome pigmentation in silkworms and butterflies.

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake)

The paper presents the first telomere-to-telomere genome assembly of matsutake, revealing genomic features and variations that provide a reference for future genetic and conservation studies.

Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging

This study compares age-associated transcriptome changes in zebrafish and rat to identify common and species-specific aging features.

ePat: extended PROVEAN annotation tool

ePat extends PROVEAN to predict pathogenicity of indels and splice variants, and process multiple variants in a single batch.

Mutations in a β-group of solute carrier gene are responsible for egg and eye coloration of the brown egg 4 (b-4) mutant in the silkworm, Bombyx mori

The paper identifies a mutation in the Bmmah gene, a β-group solute carrier gene, as responsible for the reddish-brown egg and eye coloration in the silkworm b-4 mutant.

Zebrafish Danio rerio trunk muscle structure and growth from a spatial transcriptomics perspective

This study uses spatial transcriptomics to analyze zebrafish trunk muscle structure and growth, identifying spatial gene expression patterns and developmental processes in different muscle types.

Potential silencing of gene expression by PIWI-interacting RNAs (piRNAs) in somatic tissues in mollusk

The paper investigates the role of PIWI/piRNA in somatic tissues of the pearl oyster Pinctada fucata, showing that piRNA0001 regulates hundreds of endogenous genes through differential expression.

Chromosome-level genome construction of a Japanese stickleback species using ultra-dense linkage analysis using single-cell sequencing of sperms

The paper constructs a chromosome-level genome of Gasterosteus nipponicus using ultra-dense linkage analysis from single-cell sperm sequencing data.

Designed hybrids facilitate efficient generation of high-resolution linkage maps

This paper introduces a method using hybrid organisms to generate high-resolution linkage maps at lower cost and higher density for pufferfish species.